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PDB_REDO: automated re-refinement of X-ray structure models in the PDB
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2009 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 42, 376-384 p.Article in journal (Refereed) Published
Abstract [en]

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Place, publisher, year, edition, pages
2009. Vol. 42, 376-384 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-129054DOI: 10.1107/S0021889809008784ISI: 000266268300002OAI: oai:DiVA.org:uu-129054DiVA: diva2:337515
Available from: 2010-08-06 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved

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